4WJI
Crystal structure of cyclohexadienyl dehydrogenase from Sinorhizobium meliloti in complex with NADP and tyrosine
X-RAY DIFFRACTION
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, SITTING DROP | 6.5 | 289 | 0.2 ul of 11 mg/ml protein in 20 mM HEPES pH 7.5, 150 mM NaCl, 10% Glycerol, 0.1% Sodium Azid, 0.5 mM TCEP, 7mM NADP and 20 mM tyrosine were mixed with 0.2 ul of the Index condition #83 (0.2 M Magnesium chloride hexahydrate, 0.1 M BIS-TRIS pH 6.5, 25% w/v Polyethylene glycol 3,350) and equilibrated against 1.5 M NaCl solution in 96 Well 3 drop Crystallization Plate (Swissci). Before crystallization protein was incubated with 1/50 v/v of 2 mg/ml chymotrypsin solution at 289 K for 3 hours |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.12 | 41.88 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 76.409 | α = 90 |
b = 68.891 | β = 94.34 |
c = 51.097 | γ = 90 |
Symmetry | |
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Space Group | C 1 2 1 |
Diffraction
Diffraction Experiment | ||||||||||||||
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ID # | Crystal ID | Scattering Type | Data Collection Temperature | Detector | Detector Type | Details | Collection Date | Monochromator | Protocol | |||||
1 | 1 | x-ray | 100 | CCD | MARMOSAIC 300 mm CCD | Beryllium Lenses | 2013-06-20 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | APS BEAMLINE 21-ID-G | 0.97856 | APS | 21-ID-G |
Data Collection
Overall | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (Observed) | R Merge I (Observed) | Rrim I (All) | Rpim I (All) | Net I Over Average Sigma (I) | Redundancy | Number Reflections (All) | Number Reflections (Observed) | Observed Criterion Sigma (F) | Observed Criterion Sigma (I) | B (Isotropic) From Wilson Plot | ||||||
1 | 1.4 | 50 | 95.6 | 0.066 | 0.084 | 0.052 | 14.3 | 2.3 | 49774 | -3 | 11.7 |
Highest Resolution Shell | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | Percent Possible (Observed) | R Merge I (Observed) | Rrim I (All) | Rpim I (All) | CC (Half) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | ||||||||
1 | 1.4 | 1.42 | 93.4 | 0.369 | 0.501 | 0.336 | 0.734 | 1.8 | 1.7 | 2421 |
Refinement
Statistics | |||||||||||||||||||
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Diffraction ID | Structure Solution Method | Cross Validation method | Resolution (High) | Resolution (Low) | Number Reflections (Observed) | Number Reflections (R-Free) | Percent Reflections (Observed) | R-Factor (Observed) | R-Work | R-Free | R-Free Selection Details | Mean Isotropic B | |||||||
X-RAY DIFFRACTION | SAD | THROUGHOUT | 1.4 | 50 | 49707 | 2524 | 95.6 | 0.1173 | 0.1151 | 0.1587 | RANDOM | 15.987 |
Temperature Factor Modeling | ||||||
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Anisotropic B[1][1] | Anisotropic B[1][2] | Anisotropic B[1][3] | Anisotropic B[2][2] | Anisotropic B[2][3] | Anisotropic B[3][3] | |
0.64 | -1.2 | -0.19 | -0.27 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 35.792 |
r_sphericity_free | 20.153 |
r_dihedral_angle_4_deg | 14.731 |
r_dihedral_angle_3_deg | 12.019 |
r_sphericity_bonded | 11.494 |
r_dihedral_angle_1_deg | 4.853 |
r_rigid_bond_restr | 4.816 |
r_mcangle_it | 2.219 |
r_mcbond_it | 1.802 |
r_mcbond_other | 1.801 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 2162 |
Nucleic Acid Atoms | |
Solvent Atoms | 276 |
Heterogen Atoms | 66 |
Software
Software | |
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Software Name | Purpose |
Blu-Ice | data collection |
HKL-3000 | data collection |
HKL-3000 | data reduction |
HKL-3000 | data scaling |
HKL-3000 | phasing |
SHELX | phasing |
DM | phasing |
REFMAC | refinement |
PDB_EXTRACT | data extraction |
SCALEPACK | data scaling |